[2017-08-24T11:10:35,855][WARN ][logstash.runner ] SIGINT received. Shutting down the agent.
[2017-08-24T11:10:35,959][WARN ][logstash.agent ] stopping pipeline {:id=>"main"}
[2017-08-24T11:10:40,902][WARN ][logstash.runner ] Received shutdown signal, but pipeline is still waiting for in-flight events
to be processed. Sending another ^C will force quit Logstash, but this may cause
data loss.
[2017-08-24T11:10:40,981][WARN ][logstash.shutdownwatcher ] {"inflight_count"=>0, "stalling_thread_info"=>{}}
[2017-08-24T11:10:40,996][ERROR][logstash.shutdownwatcher ] The shutdown process appears to be stalled due to busy or blocked plugins. Check the logs for more information.

Logstash doesn't just need to be able to read/write the config files. It also needs to have write privileges to the log file destination directory, and it needs to have read privileges for the source files you plan on reading.

I see you removed the Elasticsearch logs that showed your ES node hit the 90% full mark:

[2017-08-24T10:37:48,949][WARN ][o.e.c.r.a.DiskThresholdMonitor] [es-logger-production-node] high disk watermark [90%] exceeded on [3mLr6xKbSgKvWH7loKo9JA][es-logger-production-node][/var/lib/elasticsearch/nodes/0] free: 3.5gb[6.1%], shards will be relocated away from this node

While it may be somewhat tangential, that's not going to help. If you hit the 5% free mark, you won't be able to index anymore.